Frequently Asked Questions

For troubleshooting help, see this page

Installation

• How do I install an R package for the first time?
• Can I install Python components manually?

Usage

• What does a Giotto workflow look like?
• How do I create a Giotto analysis object?
• Is there low-level tooling for importing from popular spatial technologies?
• What are Giotto instructions?
• How do I calculate a raw expression matrix from raw features and segementations?
• How do I set up spatial bins to aggregate with?
• Is there a convenient workflow function for data processing?
• How can I build a composable pipeline for processing my data?
• What are spatial units and feature types?
• What are important Giotto functions to know?
• How do I spatially manipulate my data?
• How do I extract data out of the Giotto Object?
• How do I interactively select my data?
• What is the structure of the Giotto Object?
• How do I register spatial datasets together?
• Are there any tools for TMA data?
• How do I perform data filtering?
• How do I set up a spatial or nearest neighbor network?
• How do I find variable features?
• How do I perform dimension reduction?
• How can I detect spatially organized genes?
• How do I cluster features into modules with similar spatial expression patterns?
• How can I check for enrichment of gene/feature signatures?
• The biology I study is highly spatially organized. Can I improve my clustering?
• What can I find differentially expressed features?
• How do I use Harmony with Giotto to remove batch effects?
• How do I use HMRF?
• How do I deconvolve my data?
• How do I perform kriging to super-resolve my Visium data?
• How do I save my object?
• How do I save/export my plots?
• Is there a docker image?
• Can I use the docker image with singularity?
• How do I contribute to Giotto?
• How do I report a bug?

Data Availability

Where can I find seqFISH+ and other ready-to-use datasets?

• Checkout our GiottoData extension package to find already preprocessed datasets and Giotto mini Objects.

Where else can I find more spatial datasets?

Checkout the following for more spatial-omics data:

• Aquila
• Tencent's SODB
• PySODB, a python interface for the SODB

How can I automatically download tutorial datasets?

Use getSpatialDataset() from GiottoData:

# Ensure Giotto Suite is installed
if(!"Giotto" %in% installed.packages()) {
  pak::pkg_install("drieslab/Giotto")
}

library(Giotto)

# Ensure Giotto Data is installed
if(!"GiottoData" %in% installed.packages()) {
  pak::pkg_install("drieslab/GiottoData")
}

library(GiottoData)


# choose your directory
my_working_dir = getwd()

# merFISH example:

# standard download data to working directory
getSpatialDataset(dataset = 'merfish_preoptic', 
                  directory = my_working_dir)

# use wget to  download data to working directory (much faster)
getSpatialDataset(dataset = 'merfish_preoptic', 
                  directory = my_working_dir, 
                  method = 'wget')

# avoid certification issues with wget
getSpatialDataset(dataset = 'merfish_preoptic', 
                  directory = my_working_dir, 
                  method = 'wget', 
                  extra = '--no-check-certificate')